Hi Alexandre,
Thank you for your reply.
I tried deleting the ~/.local and ~/.cache pip related staff...but the
problem still appears.
Should I delete anything else?
Thank you again !
quim
Missatge de Strube, Alexandre <a.str...@fz-juelich.de> del dia dl., 18
d’oct. 2021 a les 23:20:
> Hi,
>
> this might happen if your pip installation is somehow messed up. I had
> this happening recently, and turns out it was pip itself, so I deleted all
> my
> pip stuff, .local , .cache and so on
>
> On 18. Oct 2021, at 14:24, Joaquim Jornet Somoza <joaquim.jor...@ehu.eus>
> wrote:
>
> Dear Alexandre,
>
> Thanks for your quick reply.
>
> Actually, I have tried to installed already with --robot option:
>
> eb Biopython-1.78-intel-2020a-Python-3.8.2.eb -r ./
>
> I don't know why the santiy_check step tries to use a functionality not
> listed on the
> dependencies section, neither installed within
> Python-3.8.2-GCCcore-9.3.0.eb.
>
> I think the error comes from the sanity_check step. This is the error in
> the log file:
>
> == 2021-10-18 12:21:38,634 build_log.py:169 ERROR EasyBuild crashed with
> an error (at
> easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124
> in __init__): `pip check` failed:
>
> yaff 1.4.2 requires h5py, which is not installed.
> (at
> *easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/easyblocks/generic/pythonpackage.py:886
> in sanity_check_step*)
>
>
> You suggested to install h5py by hand as an extension?
> I.e including in the easyconfig file for Biopython something like:
>
>
> *exts_list = [ *
>
> * ('h5py', '3.0.0', {*
>
> * 'checksums':
> ['7d3803be1b530c68c2955faba726dc0f591079b68941a0c0269b5384a42ab519'],*
> *]*
>
> Thank you !
> quim
>
> Missatge de Strube, Alexandre <a.str...@fz-juelich.de> del dia dl., 18
> d’oct. 2021 a les 13:46:
>
>> Hola Joaquim,
>>
>> dependencies are dealt with --robot setting - which should bring the
>> right ones.
>>
>> In any case, you can always install h5py beforehand yourself.
>>
>> On 18. Oct 2021, at 12:26, Joaquim Jornet Somoza <
>> j.jornet.som...@gmail.com> wrote:
>>
>> Dear easybuilders,
>>
>> I am trying to install Biopython-1.78-intel-2020a-Python-3.8.2.eb, but
>> after the installation and
>> postprocessing, the sanity check step fails.
>>
>> I have found this error that I don't know how to avoid:
>>
>> == 2021-10-18 12:21:38,634 build_log.py:169 ERROR EasyBuild crashed with
>> an error (at
>> easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124
>> in __init__): `pip check` failed:
>> yaff 1.4.2 requires h5py, which is not installed.
>>
>> Could anyone help me?
>>
>>
>> Best regards
>> quim
>>
>> --
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------
>> *Dr. Joaquim Jornet Somoza*
>> *Técnico Superior de Cálculo Científico *
>> Servicios Generales a la Investigación (*SGIker*)
>> Universidad del País Vasco (*UPV/EHU*)
>> email: j.jornet.som...@gmail.com
>> Edificio Joxe Maria Korta (Campus Gipuzkoa)
>> Av. Tolosa 72, 4a planta
>> 20018 Donostia-San Sebastián,
>> Gipuzkoa, Spain
>>
>> *External Collaborator.*
>> Nano-Bio Spectroscopy group
>> Departamento de Física de Materiales
>> Universidad del País Vasco (UPV/EHU)
>> Donostia-San Sebastián, Gipuzkoa, Spain
>>
>> The Max Planck Institute for the Structure and Dynamics of Matter (MPSD)
>> Bldg. 99 (CFEL)
>> Luruper Chaussee 149
>> 22761 Hamburg, Germany
>>
>>
>>
>
> --
>
> ----------------------------------------------------------------------------------------------------------------------------------------
> *Dr. Joaquim Jornet Somoza*
> *Técnico Superior de Cálculo Científico *
> Servicios Generales a la Investigación (*SGIker*)
> Universidad del País Vasco (*UPV/EHU*)
> email: joaquim.jor...@ehu.eus
> Edificio Joxe Maria Korta (Campus Gipuzkoa)
> Av. Tolosa 72, 4a planta
> 20018 Donostia-San Sebastián,
> Gipuzkoa, Spain
> w: http://www.ehu.es/sgi/
> tw: @izosgi
> fb: izosgi
>
>
>
--
----------------------------------------------------------------------------------------------------------------------------------------
*Dr. Joaquim Jornet Somoza*
*Técnico Superior de Cálculo Científico *
Servicios Generales a la Investigación (*SGIker*)
Universidad del País Vasco (*UPV/EHU*)
email: j.jornet.som...@gmail.com
Edificio Joxe Maria Korta (Campus Gipuzkoa)
Av. Tolosa 72, 4a planta
20018 Donostia-San Sebastián,
Gipuzkoa, Spain
*External Collaborator.*
Nano-Bio Spectroscopy group
Departamento de Física de Materiales
Universidad del País Vasco (UPV/EHU)
Donostia-San Sebastián, Gipuzkoa, Spain
The Max Planck Institute for the Structure and Dynamics of Matter (MPSD)
Bldg. 99 (CFEL)
Luruper Chaussee 149
22761 Hamburg, Germany
